Brain-indexer

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**Features**
* Support `morphio.Collection` to be able to also read from morphology
containers.

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We've removed one method. It seems unlikely that users would be affected by
this. Migration instructions are provided in the corresponding bullet point.

**Features**
* CLI supports `--verbose` which prints log messages of any severity.
* Infrastructure for creating indexes with randomly placed elements.
* Support adding spheres to in-memory `SphereIndex`.
* Support indexes of points `PointIndex`.

**Improvements**
* Create in-memory indexes "in bulk". The internal structure of an R-tree is
much better if all elements are known upfront; as opposed to being inserted
one-by-one. This commit ensures that in-memory indexes are created via bulk
creation.

It optionally, old in-memory indexes should be recreated to benefit from
this optimization. However, old indexes can still be read. Multi-indexes
aren't affected at all by this change.

* Use `std::filesystem` instead of `boost::filesystem`.

* General restructuring of code and CI.

* Added test to ensure consistency of morphology IDs between BrainIndexer and
`libsonata`.

**Deprecation**
* We've deprecated the certain constructors of `core.MorphIndex` and
`core.SynapseIndex`. Users of BrainIndexer aren't expected to be using
these classes directly.

**Removal**
* We've removed a method `add_sphere` from the `SphereBuilder`. Instead
please create all spheres upfront and then create the index. If upfront
creation of all spheres doesn't work, the in-memory `SphereIndex` supports
adding spheres interatively.

**Fixes**
* Improved error message for missing files.
* Warn if in-memory indexes are large.
* Improved documentation.
* Progress bar is only shown when in a TTY.

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**December 2022**

**Improvements**
* Fix publishing documentation.

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**December 2022**

**Features**
* Ability to optimize the order in which queries should be performed to
improve cache reuse of multi-indexes.

**Improvements**
* Document BrainIndexer environment variables.
* Document important performance tricks.
* Fix morphology builder to return SONATA enabled indexes.
* Relax the minimum number of synapses in a multi-index.
* Improvements to the overall code quality.

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**November 2022**

**Features**
* Integrates ``section_type`` in index. This allows to retrieve information on the
type of section (i.e. ``soma``, ``axon``, ``basal_dendrite``, ``apical_dendrite``)
directly from the query.
* Add ``box_empty`` and ``sphere_empty`` functions to check if a specific area is empty.

**Improvements**
* Ignore ``virtual`` populations in circuit config files.
* Populations with unsupported types are not allowed anymore.
* Relaxed requirement on number of MPI ranks: now can be in the form ``2**n * 3**m * 5**l + 1``.
* Workaround for ``BOOST_STATIC_CONSTANT`` build issue.
* Multiple improvements to CI.
* Removed memory mapped files support entirely.
* Multiple fixes and improvements to the implementation.

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**October 2022**

No changes since version ``0.9.0``.